High latitude freshwater systems are facing changes in catchment-mediated allochthonous input, as well as physical and chemical controls triggered by on-going climate change, which may alter their carbon processing and ecological characteristics. To explore changes in chironomid functional responses and carbon utilization in relation to long-term environmental change, we studied a sediment core covering ca. 2000 years from a tundra lake in northern Finland, which was analysed for sediment geochemistry, isotopic composition of chironomid remains and their functional assemblages. We aimed to relate changes in chironomid functional feeding assemblages and resource utilization, based on Bayesian stable isotope modelling, and determined that the long-term resource utilization was more controlled by sediment geochemistry (resource availability) and climatic variables, reflecting changes in habitat and lake ontogeny, rather than the functional feeding assemblage composition. Change horizons were observed for both sediment geochemistry and functional assemblage composition. However, different timing of these changes suggests different drivers affecting the dynamics of primary production and chironomid community functionality. We also compared the recent warming period to Medieval Climate Anomaly (MCA), observing divergent patterns, which suggests that MCA may not be a good analogue for changes induced by on-going climate warming.